def species_to_fix(ssn, binomial, author, create=False):
if binomial.find(' ') == -1:
return None
binomial = utils.to_unicode(binomial)
author = utils.to_unicode(author)
gen_epithet, sp_epithet = binomial.split(' ', 1)
return Species.retrieve_or_create(
ssn, {'object': 'taxon',
'rank': 'species',
'ht-epithet': gen_epithet,
'epithet': sp_epithet,
'ht-rank': 'genus',
'author': author},
create=create)
def species_to_fix(ssn, binomial, author, create=False):
if binomial.find(' ') == -1:
return None
binomial = utils.to_unicode(binomial)
author = utils.to_unicode(author)
gen_epithet, sp_epithet = binomial.split(' ', 1)
return Species.retrieve_or_create(
ssn, {'object': 'taxon',
'rank': 'species',
'ht-epithet': gen_epithet,
'epithet': sp_epithet,
'ht-rank': 'genus',
'author': author},
create=create)
def on_frame2_next(self, *args):
"execute all that is selected in liststore2 and move to frame 3"
self.on_frame_next(*args)
tb = self.view.widgets.textbuffer3
tag_bold = tb.create_tag(None, weight=pango.WEIGHT_BOLD)
tag_red = tb.create_tag(None, weight=pango.WEIGHT_BOLD, foreground=pango.Color("red"))
tb.set_text("")
for row in self.tick_off_list:
if row[TO_PROCESS] is False:
tb.insert_at_cursor("skipping %s\n" % (row[OLD_BINOMIAL] or row[NEW_BINOMIAL]))
continue
if row[OLD_BINOMIAL] == "":
tb.insert_with_tags(tb.get_end_iter(), "new taxon %s" % row[NEW_BINOMIAL], tag_bold)
obj = species_to_fix(self.session, row[NEW_BINOMIAL], row[AUTHORSHIP], create=True)
else:
if row[TAXON_STATUS] == "Synonym":
accepted = species_to_fix(
self.session, row[ACCEPTED_BINOMIAL], row[ACCEPTED_AUTHORSHIP], create=True
)
else:
accepted = None
obj = species_to_fix(self.session, row[OLD_BINOMIAL], row[AUTHORSHIP], create=False)
if obj is None:
tb.insert_with_tags(tb.get_end_iter(), "bad taxon %s" % row[OLD_BINOMIAL], tag_bold, tag_red)
continue
tb.insert_with_tags(tb.get_end_iter(), "update taxon %s" % row[OLD_BINOMIAL], tag_bold)
gen_epithet, sp_epithet = utils.to_unicode(row[NEW_BINOMIAL]).split(" ", 1)
obj.genus.genus = gen_epithet
obj.sp = sp_epithet
if accepted:
obj.accepted = accepted
tb.insert_with_tags(tb.get_end_iter(), " %s\n" % row[AUTHORSHIP], tag_bold)
def default_completion_cell_data_func(column, renderer, model, treeiter,
data=None):
'''
the default completion cell data function for
GenericEditorView.attach_completions
'''
v = model[treeiter][0]
renderer.set_property('markup', utils.to_unicode(v))
def species_to_fix(ssn, binomial, author, create=False):
if binomial.find(" ") == -1:
return None
binomial = utils.to_unicode(binomial)
author = utils.to_unicode(author)
gen_epithet, sp_epithet = binomial.split(" ", 1)
return Species.retrieve_or_create(
ssn,
{
"object": "taxon",
"rank": "species",
"ht-epithet": gen_epithet,
"epithet": sp_epithet,
"ht-rank": "genus",
"author": author,
},
create=create,
)
def next(self):
row = self.reader.next()
t = {}
for k, v in row.iteritems():
if v == '':
t[k] = None
else:
t[k] = utils.to_unicode(v, self.encoding)
return t
def next(self):
row = self.reader.next()
t = {}
for k, v in row.iteritems():
if v == '':
t[k] = None
else:
t[k] = utils.to_unicode(v, self.encoding)
return t
def on_frame2_next(self, *args):
'execute all that is selected in liststore2 and move to frame 3'
self.on_frame_next(*args)
tb = self.view.widgets.textbuffer3
tag_bold = tb.create_tag(None, weight=pango.WEIGHT_BOLD)
tag_red = tb.create_tag(None,
weight=pango.WEIGHT_BOLD,
foreground=pango.Color('red'))
tb.set_text('')
for row in self.tick_off_list:
if row[TO_PROCESS] is False:
tb.insert_at_cursor("skipping %s\n" %
(row[OLD_BINOMIAL] or row[NEW_BINOMIAL]))
continue
if row[OLD_BINOMIAL] == '':
tb.insert_with_tags(tb.get_end_iter(),
"new taxon %s" % row[NEW_BINOMIAL],
tag_bold)
obj = species_to_fix(self.session,
row[NEW_BINOMIAL],
row[AUTHORSHIP],
create=True)
else:
if row[TAXON_STATUS] == 'Synonym':
accepted = species_to_fix(self.session,
row[ACCEPTED_BINOMIAL],
row[ACCEPTED_AUTHORSHIP],
create=True)
else:
accepted = None
obj = species_to_fix(self.session,
row[OLD_BINOMIAL],
row[AUTHORSHIP],
create=False)
if obj is None:
tb.insert_with_tags(tb.get_end_iter(),
"bad taxon %s" % row[OLD_BINOMIAL],
tag_bold, tag_red)
continue
tb.insert_with_tags(tb.get_end_iter(),
"update taxon %s" % row[OLD_BINOMIAL],
tag_bold)
gen_epithet, sp_epithet = utils.to_unicode(
row[NEW_BINOMIAL]).split(' ', 1)
obj.genus.genus = gen_epithet
obj.sp = sp_epithet
if accepted:
obj.accepted = accepted
tb.insert_with_tags(tb.get_end_iter(), " %s\n" % row[AUTHORSHIP],
tag_bold)
def writerow(self, row):
"""
Write a row. If row is a dict then row.values() is written
and therefore care should be taken to ensure that row.values()
returns a consisten order.
"""
if isinstance(row, dict):
row = row.values()
t = []
for s in row:
if s == None:
t.append(None)
else:
t.append(utils.to_unicode(s, self.encoding))
self.writer.writerow(t)
def writerow(self, row):
"""
Write a row. If row is a dict then row.values() is written
and therefore care should be taken to ensure that row.values()
returns a consisten order.
"""
if isinstance(row, dict):
row = row.values()
t = []
for s in row:
if s is None:
t.append(None)
else:
t.append(utils.to_unicode(s, self.encoding))
self.writer.writerow(t)
def to_python(self, value):
if value in (u'', '', None):
return None
return utils.to_unicode(value, self.encoding)
def to_python(self, value):
if not value.strip():
return ''
return utils.to_unicode(value, self.encoding)